This document contains all the information required to complete the virtual field course. In this course we will carry out a series of virtual point counts using real sound recordings collected from point counts completed high in the Colombian Andes. At each point we will record the bird species that we think are present, and then, once we have completed all the point counts, we will compare how communities vary between pasture and forest points. Because you are unlikely to be able to identify Colombian birds from their song, rather than recording real species, we will instead record “morphospecies”, which we can think of as distinct vocalisations that we think are likely to be made by different species. If we were doing this by eye, rather than by sound, it might be something like “I saw a medium-sized red bird with a heavy beak, a blue and black bird with some yellow on the wing, and a large bright green bird with a big bill”. Without knowing the true species these represent, we can still use these descriptions to record them each time they crop up. Here we will do the same, but with the vocalisations (this will start to make more sense as we work through the recordings).
This zip file contains all the code and files that you need for this practical, so go ahead and download it now. The practical.zip file you have just downloaded is a .zip file, which is just a way of compressing all the data to create a file with a smaller filesize. Before doing anything else, we need to first unzip it to retain the original files. If you right click on the practical.zip that you have downloaded, you will have a list of options, and you need to select ‘Extract all’. By default it will extract all the files to the directory that the zip file is in: this is fine, but if you would like to save the files somewhere in particular, you can also specify a different directory at this stage. When it has done this you should be able to see a practical folder that, unlike the zipped version, no longer has a zip across the thumbnail.
Important: Make sure you do the unzipping above: you will have problems down the line otherwise. If you aren’t sure, ask!
In the files directory you will fine a template_datatable file, both as a .csv and a .xlsx. Open up whichever one you feel like (they are the same, but the csv version has obviously dropped the excel-specific formatting).
Important: You need to make sure that you don’t alter the formatting of this datafile. There are 11 columns for you to enter information into, and 45 rows (not including the header). There are more rows than there are species in the recordings, so you don’t need to add any rows. You also don’t need to edit the morphospecies column, nor should you remove any rows. It is important that you only put numbers in the point columns. If there isn’t a particular species on a particular point, just leave the cell empty. Try to avoid accidentally putting spaces (" “) in cells you aren’t using, and don’t add any additional columns. You can put whatever you want in the notes column (it might help, for example, to record some notes about the sound of a particular morphospecies, e.g. ”high te-te-te-te“, or”descending series of notes"). If you do accidentally do any of these things, you might struggle to read the data into R.
When we have come to the end of the listening section of this practical, you need to save your completed datatable as completed_datatable.csv, in the files directory (the same place you read the template version in from). Note that you have to save it as a .csv file, with the correct name and in the correct location: you won’t be able to read it in if you don’t do this. To save as a .csv, click ‘Save as’, navigate to the files directory, and in the ’Save as type` option, scroll down to ’CSV (Comma delimited) (*.csv)’.
Important: If you aren’t sure how to save the file correctly, just ask a demonstrator. It can be quite tricky to debug your code if you go off-piste at this stage!
You can listen to the soundfiles here directly, but if you are struggling to play them for some reason, they are also provided in the zip file, in the sound_files directory. We are now going to travel around all of our point counts, listening to each of the recordings and noting the species that we think are present on each point, and how many of them we think there are.
Point 1
Point 2
Point 3
Point 4